Both attempts ran into problems including low amounts of food and oxygen, die-offs of many animals and plants included in the experiment (though this was anticipated since the project used a strategy of deliberately "species-packing" anticipating losses as the biomes developed), group dynamic tensions among the resident crew, outside politics, and a power struggle over management and direction of the project.

[7] Construction was carried out between 1987 and 1991 by Space Biosphere Ventures, a joint venture whose principal officers were John P. Allen, inventor and executive chairman; Margaret Augustine, CEO; Marie Harding, vice-president of finance; Abigail Alling, vice president of research; Mark Nelson, director of space and environmental applications, William F. Dempster, director of system engineering, and Norberto Alvarez-Romo, vice president of mission control.

[9][10] The window seals and structures had to be designed to be almost perfectly airtight, such that the air exchange would be extremely low, permitting tracking of subtle changes over time.

[14] Since opening a window was not an option, the structure also required a sophisticated system to regulate temperatures within desired parameters, which varied for the different biomic areas.

[16] The agricultural system produced 83% of the total diet, which included crops of bananas, papayas, sweet potatoes, beets, peanuts, lablab and cowpea beans, rice, and wheat.

Calculations indicated that Biosphere 2's farm was amongst the highest producing in the world "exceeding by more than five times that of the most efficient agrarian communities of Indonesia, southern China, and Bangladesh".

[22] Some of the domestic animals that were included in the agricultural area during the first mission included: four African pygmy goat does and one billy; 35 hens and three roosters (a mix of Indian jungle fowl (Gallus gallus), Japanese silky bantam, and a hybrid of these); two sows and one boar Ossabaw dwarf pigs; and tilapia fish grown in a rice and azolla pond system originating millennia ago in China.

Rainforest pioneer species grew rapidly, but trees there and in the savannah suffered from etiolation and weakness caused by lack of stress wood, normally created in response to winds in natural conditions.

[28] The planned ecological succession in the rainforest and strategies to protect the area from harsh incident sunlight and salt aerosols from the ocean worked well, and a surprising amount of the original biodiversity persisted.

[34] Before the first closure mission was half over, the group had split into two factions and, according to Poynter, people who had been intimate friends had become implacable enemies, barely on speaking terms.

"[37] The factions inside the bubble formed from a rift and power struggle between the joint venture partners on how the science should proceed, as biospherics or as specialist ecosystem studies (perceived as reductionist).

[38] Time magazine wrote: "Now, the veneer of credibility, already bruised by allegations of tamper-prone data, secret food caches and smuggled supplies, has cracked ... the two-year experiment in self-sufficiency is starting to look less like science and more like a $150 million stunt.

[42] The Alling faction feared that the Poynter group were prepared to go so far as to import food, if it meant making them fitter to carry out research projects.

[46] Among the problems and miscalculations encountered in the first mission were unanticipated condensation making the "desert" too wet, population explosions of greenhouse ants and cockroaches, morning glories overgrowing the rainforest area blocking out other plants, and less sunlight (40–50% of outside light) entering the facility than originally anticipated.

[49] Some thought that these criticisms ignored that Biosphere 2 was an experiment where the unexpected would occur, adding to knowledge of how complex ecologies develop and interact, not a demonstration where everything was known in advance.

[50] H. T. Odum noted: "The management process during 1992–1993 using data to develop theory, test it with simulation, and apply corrective actions was in the best scientific tradition.

[52] Since some biospherians were starting to have symptoms like sleep apnea and fatigue, Walford and the medical team decided to boost oxygen with injections in January and August 1993.

Daily fluctuation of carbon dioxide dynamics was typically 600 ppm because of the strong drawdown during sunlight hours by plant photosynthesis, followed by a similar rise during the nighttime when system respiration dominated.

The crew worked to manage the CO2 by occasionally turning on a CO2 scrubber, after realizing that activating and de-activating the desert and savannah through control of irrigation water, cutting and storing biomass to sequester carbon, and utilizing all potential planting areas with fast-growing species to increase system photosynthesis, wouldn't be enough to sustain human life.

[54] In November 1991, investigative reporting in The Village Voice alleged that the crew had secretly installed the CO2 scrubber device, and claimed that this violated Biosphere 2's advertised goal of recycling all materials naturally.

Subsequent research showed that Biosphere 2's farm soils had reached a more stable ratio of carbon and nitrogen, lowering the rate of CO2 release, by 1998.

[57] The respiration rate was faster than the photosynthesis (possibly in part due to relatively low light penetration through the glazed structure and the fact that Biosphere 2 started with a small but rapidly increasing plant biomass) resulting in a slow decrease of oxygen.

[58] After Biosphere 2's first mission, extensive research and system improvements were undertaken, including sealing concrete to prevent the uptake of carbon dioxide.

[5] On April 1, 1994, a severe dispute within the management team led to the ousting of the on-site management by federal marshals serving a restraining order, and financier Ed Bass hired Steve Bannon, then-manager of the Bannon & Co. investment banking team from Beverly Hills, California, to run Space Biospheres Ventures.

"[62] About 10% of the Biosphere's air was exchanged with the outside during this time, according to systems analyst Donella Meadows, who received a communication from Alling saying that she and Van Thillo judged it their ethical duty to give those inside the choice of continuing with the drastically changed human experiment or leaving, as they didn't know what the crew had been told of the new situation.

[64] Leading managers of Biosphere 2 from the original founding group stated both abusive behaviour by Bannon and others, and that the bankers' actual goal was to destroy the experiment.

[77] Abigail Alling, Mark van Thillo and Sally Silverstone helped start the Biosphere Foundation where they worked on coral reef and marine conservation and sustainable agricultural systems.

[80] He was referring to the Synergia Ranch in New Mexico, where indeed many of the Biospherians did practice theater under John Allen's leadership, and began to develop the ideas behind Biosphere 2.

[90] Research during Columbia's tenure demonstrated the devastating impacts on coral reefs from elevated atmospheric CO2 and acidification that will result from continued global climate change.

[94] In June 2007, the site was sold for $50 million to CDO Ranching & Development, L.P. 1,500 houses and a resort hotel were planned, but the main structure was still to be available for research and educational use.